Yes. The
disabled_storage_engines
configuration option defines which storage engines cannot be
used to create tables or tablespaces. By default,
disabled_storage_engines is
empty (no engines disabled), but it can be set to a
comma-separated list of one or more engines.

A.2.5.

Is there an advantage to using the InnoDB
storage engine exclusively, as opposed to a combination of
InnoDB and non-InnoDB
storage engines?

Yes. Using InnoDB tables exclusively can
simplify backup and recovery operations. MySQL Enterprise Backup
does a hot backup of all
tables that use the InnoDB storage engine.
For tables using MyISAM or other
non-InnoDB storage engines, it does a
“warm” backup, where the database continues to run,
but those tables cannot be modified while being backed up. See
Section 29.2, “MySQL Enterprise Backup Overview”.